Solution given by Rice in another Thread
If using DirectX, you can use COPY instead of FLIP to stop flashing. This is an easiest solution, but will be slow since fullscreen is mean to use FLIP.

To stop flashing, you need to choose the best "Frame update at" option for the game since your game may not be set in the INI. You at least need to use "Frame Update At" = "At VI origin changes". You may want to try other values of this option for different games.